The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

TLDR

Autotrophic ammonia oxidation occurs in acid soils, despite isolated ammonia‑oxidizing bacteria failing to grow below neutral pH. The study examined whether archaea with amoA genes drive autotrophic nitrification in acid soils by profiling bacterial and archaeal community structure and phylogeny across a pH gradient (4.9–7.5) using 16S rRNA and amoA DGGE and sequencing. Community structure was profiled by 16S rRNA and amoA DGGE and sequencing, and short‑term activity was assessed by DGGE of gene transcripts in microcosms of acidic, neutral, or pH‑adjusted mixed soils. Results showed that archaeal and bacterial ammonia oxidizer communities and their gene and transcript abundances varied with soil pH, with archaeal amoA abundance decreasing as pH rose, bacterial amoA transcripts increasing, and microcosm activity revealing that communities adapted to their native pH had higher relative activity, indicating distinct physiological traits and ecological niches that influence nitrification in acid.

Abstract

Summary Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9–7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amo A genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short‐term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils.